bioRxiv preprint doi: https://doi.org/10.1101/2021.04.04.438367; this version posted April 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A translation control module coordinates germline stem cell differentiation with 2 ribosome biogenesis during Drosophila oogenesis 3 Elliot T. Martin1*, Patrick Blatt1*, Elaine Ngyuen2, Roni Lahr2, Sangeetha Selvam1, Hyun Ah M. 4 Yoon1,3, Tyler Pocchiari1,4, Shamsi Emtenani5, Daria E. Siekhaus5, Andrea Berman2, Gabriele 5 Fuchs1† and Prashanth Rangan1† 6 1Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 7 12202 8 2Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 9 3Albany Medical College, Albany, NY 12208 10 4SUNY Upstate Medical University, Syracuse, NY 13210-2375 11 5Institute of Science and Technology Austria, Klosterneuburg, Austria 12 *These authors contributed equally to this work 13 †Co-corresponding authors 14 Email: [email protected], [email protected] 15 Summary: Ribosomal defects perturb stem cell differentiation, causing diseases called 16 ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, 17 we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila 18 oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant 19 stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is 20 required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine 21 (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, 22 Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related 23 mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP- 24 motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif 25 in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal 26 proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation. 27 Introduction 28 All life depends on the ability of ribosomes to translate mRNAs into proteins. Despite this universal 29 requirement, ribosome biogenesis is not universally equivalent. Stem cells, the unique cell type 30 that underlies the generation and expansion of tissues, in particular have a distinct ribosomal 31 requirement (Gabut et al., 2020; Sanchez et al., 2016; Woolnough et al., 2016; Zahradkal et al., 32 1991; Zhang et al., 2014). Ribosome production and levels are dynamically regulated to maintain 33 higher amounts in stem cells (Fichelson et al., 2009; Gabut et al., 2020; Sanchez et al., 2016; 34 Woolnough et al., 2016; Zahradkal et al., 1991; Zhang et al., 2014). For example, ribosome 35 biogenesis components are often differentially expressed, as observed during differentiation of 36 embryonic stem cells, osteoblasts, and myotubes (Gabut et al., 2020; Watanabe-Susaki et al., 37 2014; Zahradkal et al., 1991). In some cases, such as during Drosophila germline stem cell (GSC) 38 division, ribosome biogenesis factors asymmetrically segregate during asymmetric cell division, 39 such that a higher pool of ribosome biogenesis factors is maintained in the stem cell compared to 40 the daughter cell (Blatt et al., 2020a; Fichelson et al., 2009; Zhang et al., 2014). Reduction of 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.04.438367; this version posted April 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 41 ribosome levels in several stem cells systems can cause differentiation defects (Corsini et al., 42 2018; Fortier et al., 2015; Khajuria et al., 2018; Zhang et al., 2014). In Drosophila, perturbations 43 that reduce ribosome levels in the GSCs result in differentiation defects causing infertility 44 (Sanchez et al., 2016). Similarly, humans with reduced ribosome levels are afflicted with clinically 45 distinct diseases known as ribosomopathies, such as Diamond-Blackfan anemia, that often result 46 from loss of proper differentiation of tissue-specific progenitor cells (Armistead and Triggs-Raine, 47 2014; Barlow et al., 2010; Brooks et al., 2014; Higa-Nakamine et al., 2012; Lipton et al., 1986; 48 Mills and Green, 2017). However, the mechanisms by which ribosome biogenesis is coupled to 49 proper stem cell differentiation remain incompletely understood. 50 Ribosome production requires the transcription of ribosomal RNAs (rRNAs) and of mRNAs 51 encoding ribosomal proteins (Bousquet-Antonelli et al., 2000; de la Cruz et al., 2015; Granneman 52 et al., 2011, 2006; Tafforeau et al., 2013; Venema et al., 1997). Several factors, such as helicases 53 and endonucleases, transiently associate with maturing rRNAs to facilitate rRNA processing, 54 modification, and folding (Granneman et al., 2011; Sloan et al., 2017; Tafforeau et al., 2013; 55 Watkins and Bohnsack, 2012). Ribosomal proteins are imported into the nucleus, where they 56 assemble with rRNA to form the small 40S and large 60S ribosome subunits, which are then 57 exported to the cytoplasm (Baxter-Roshek et al., 2007; Decatur and Fournier, 2002; Granneman 58 et al., 2011, 2006; Koš and Tollervey, 2010; Nerurkar et al., 2015; Tafforeau et al., 2013; Zemp 59 and Kutay, 2007). Loss of RNA Polymerase I transcription factors, helicases, exonucleases, large 60 or small subunit ribosomal proteins, or other processing factors all compromise ribosome 61 biogenesis and trigger diverse stem cell-related phenotypes (Brooks et al., 2014; Calo et al., 2018; 62 Mills and Green, 2017; Sanchez et al., 2016; Yelick and Trainor, 2015; Zhang et al., 2014). 63 Nutrient availability influences the demand for de novo protein synthesis and thus ribosome 64 biogenesis (Anthony et al., 2000; Hong et al., 2012; Mayer and Grummt, 2006; Shu et al., 2020). 65 In mammals, nearly all of the mRNAs that encode the ribosomal proteins contain a Terminal Oligo 66 Pyrimidine (TOP) motif within their 5’ untranslated region (UTR), which regulates their translation 67 in response to nutrient levels (Fonseca et al., 2015; Hong et al., 2017; Lahr et al., 2017; 68 Tcherkezian et al., 2014). Under growth-limiting conditions, La related protein 1 (Larp1) binds to 69 the TOP sequences and to mRNA caps to inhibit translation of ribosomal proteins (Fonseca et 70 al., 2015; Jia et al., 2021; Lahr et al., 2017; Philippe et al., 2018). When growth conditions are 71 suitable, Larp1 is phosphorylated by the nutrient/redox/energy sensor mammalian Target of 72 rapamycin (mTOR) complex 1 (mTORC1), and does not efficiently bind the TOP sequence, thus 73 allowing for efficient translation of ribosomal proteins (Fonseca et al., 2018, 2015; Hong et al., 74 2017; Jia et al., 2021). In some instances, Larp1 binding can also stabilize TOP-containing 75 mRNAs (Aoki et al., 2013; Berman et al., 2020; Gentilella et al., 2017; Ogami et al., 2020), linking 76 mRNA translation with mRNA stability to promote ribosome biogenesis (Aoki et al., 2013; Berman 77 et al., 2020; Fonseca et al., 2018, 2015; Hong et al., 2017; Lahr et al., 2017; Ogami et al., 2020; 78 Philippe et al., 2018). Cellular nutrient levels are known to affect stem cell differentiation and 79 oogenesis in Drosophila (Hsu et al., 2008), however whether TOP motifs exist in Drosophila to 80 coordinate ribosome protein synthesis is unclear. The Drosophila ortholog of Larp1, La related 81 protein (Larp) is required for proper cytokinesis and meiosis in Drosophila testis as well as for 82 female fertility, but its targets remain undetermined (Blagden et al., 2009; Ichihara et al., 2007). 83 Germline depletion of ribosome biogenesis factors manifests as a stereotypical GSC 84 differentiation defect during Drosophila oogenesis (Sanchez et al., 2016). Female Drosophila 85 maintain 2-3 GSCs in the germarium (Figure 1A) (Kai et al., 2005; Twombly et al., 1996; Xie, 86 2000; Xie and Li, 2007; Xie and Spradling, 1998). Asymmetric cell division of GSCs produces a 87 self-renewing daughter GSC, and a differentiating daughter, called the cystoblast (CB) (Chen and 88 McKearin, 2003; McKearin and Ohlstein, 1995). This asymmetric division is unusual: following 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.04.438367; this version posted April 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 89 mitosis, the abscission of the GSC and CB is not completed until the following G2 phase (Figure 90 1A’) (De Cuevas and Spradling, 1998; Hsu et al., 2008). The GSC is marked by a round structure 91 called the spectrosome, which elongates and eventually bridges the GSC and CB, similar to the 92 fusomes that connect differentiated cysts (Figure 1A’). During abscission the extended 93 spectrosome structure is severed and a round spectrosome is established in the GSC and the 94 CB (De Cuevas and Spradling, 1998; Hsu et al., 2008). Ribosome biogenesis defects result in 95 failed GSC-CB abscission, causing cells to accumulate as interconnected cysts marked by a 96 fusome-like structure called “stem cysts” (Figure 1A’) (Mathieu et al., 2013; Sanchez et al., 2016). 97 In contrast with differentiated cysts (McKearin and Ohlstein, 1995; McKearin and Spradling, 1990; 98 Ohlstein and McKearin, 1997), these stem cysts lack expression of the differentiation factor Bag 99 of Marbles (Bam), do not differentiate, and typically die, resulting in sterility (Sanchez et al., 2016).